Quote:
Originally Posted by higear223
Stock needles make it worse.
Anybody want to buy a Ninja 250? Runs great above 2500 rpm!
Need to sell for something fuel injected. 
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OK - that's a start. Are the Dynojet needles thinner and more tapered (richer) than the original ones?
I assume you have already gone back to the Dynojet needles.
So, as you let the clutch out and begin to open the throttle, does it pull cleanly and smoothly for a time, then stumble as it hits 2500? When it does begin to stumble, what amount of throttle opening are you at? Does the engine speed ever hang-up when you open the throttle and close it quickly? Could you have a vacuum leak?
If you use RPMs to adjust the idle mixture, I like to get the highest RPM - then go 1/8 to 1/4 richer. For the Ninja, richer is "out". If you're in the 2 to 3 turn out range, I would say the Pilot Jet is correct.
With that pretty close, and with your experience with the needle, I would look at the Main Jet. I would go with basic jetting numbers for your set-up - but ditch the Dynojet jets and go with OEMs.
If the Dynojet needles are richer, and they are better than the originals, I would say the Main Jet that is it in it now is too lean. You can also add some choke (enrichener) when the engine is hot (and stumbling) to see if the added fuel make the condition better or worse.